Publications

Variational Autoencoding Discrete Diffusion with Enhanced Dimensional Correlations Modeling
Tianyu Xie, Shuchen Xue, Zijin Feng, Tianyang Hu, Jiacheng Sun, Zhenguo Li, Cheng Zhang.
International Conference on Learning Representations (ICLR), 2026
[Paper]

Provable Sample-Efficient Transfer Learning Conditional Diffusion Models via Representation Learning
Ziheng Cheng, Tianyu Xie, Shiyue Zhang, Cheng Zhang.
Advances in Neural Information Processing Systems (NeurIPS), 2025
[Paper]

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference
Tianyu Xie, Yicong Mao, Cheng Zhang.
PLOS Computational Biology, 21(12), 2025
[Paper] [Code]

Continuous Semi-Implicit Models
Longlin Yu, Jiajun Zha, Tong Yang, Tianyu Xie, Xiangyu Zhang, S.-H. Gary Chan, Cheng Zhang.
International Conference on Machine Learning (ICML), 2025
[Paper] [Code]

Any-Order GPT as Masked Diffusion Model: Decoupling Formulation and Architecture
Shuchen Xue, Tianyu Xie, Tianyang Hu, Zijin Feng, Jiacheng Sun, Kenji Kawaguchi, Zhenguo Li, Zhi-Ming Ma.
Proceedings of the ES-FoMo III Workshop (oral) at the International Conference on Machine Learning (ICML), 2025
[Paper] [Code]

PhyloVAE: Unsupervised Learning of Phylogenetic Trees via Variational Autoencoders
Tianyu Xie, Harry Richman, Jiansi Gao, Frederick A Matsen IV, Cheng Zhang.
International Conference on Learning Representations (ICLR), 2025
[Paper] [Code]

Diffusion-PINN Sampler
Zhekun Shi, Longlin Yu, Tianyu Xie, Cheng Zhang.
Preprint, arXiv:2410.15336, 2024
[Paper]

Improving Tree Probability Estimation with Stochastic Optimization and Variance Reduction
Tianyu Xie$^\ast$, Musu Yuan$^\ast$, Minghua Deng, Cheng Zhang.
Statistics and Computing, 34(186), 2024
[Paper] [Code]

Variational Bayesian Phylogenetic Inference with Semi-implicit Branch Length Distributions
Tianyu Xie, Frederick A Matsen IV, Marc A Suchard, Cheng Zhang.
Preprint, arXiv:2408.05058, 2024
[Paper] [Code]

Reflected Flow Matching
Tianyu Xie$^\ast$, Yu Zhu$^\ast$, Longlin Yu$^\ast$, Tong Yang, Ziheng Cheng, Shiyue Zhang, Xiangyu Zhang, Cheng Zhang.
International Conference on Machine Learning (ICML), 2024
[Paper] [Code]

Kernel Semi-Implicit Variational Inference
Ziheng Cheng$^\ast$, Longlin Yu$^\ast$, Tianyu Xie, Shiyue Zhang, Cheng Zhang.
International Conference on Machine Learning (ICML), 2024
[Paper] [Code]

Hierarchical Semi-Implicit Variational Inference with Application to Diffusion Model Acceleration
Longlin Yu$^\ast$, Tianyu Xie$^\ast$, Yu Zhu$^\ast$, Tong Yang, Xiangyu Zhang, Cheng Zhang.
Advances in Neural Information Processing Systems (NeurIPS), 2023
[Paper] [Code]

ARTree: A Deep Autoregressive Model for Phylogenetic Inference
Tianyu Xie, Cheng Zhang.
Advances in Neural Information Processing Systems (NeurIPS, spotlight), 2023
[Paper] [Code]